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Install bifti in playground notebooks that use --no-deps - #204

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claude/confident-wozniak-old4ba
Oct 28, 2026
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J-Endres merged 2 commits into
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claude/confident-wozniak-old4ba

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MRzeroCore 1.3 added bifti as a dependency. The playground notebooks that run pip install MRzeroCore --no-deps don't get it, so they break.

This PR adds !pip install bifti --no-deps right after the MRzeroCore install in the 18 notebooks that use --no-deps. Where the original line had &> /dev/null, the new line keeps it.

bifti is installed with --no-deps too. Its requirements are numpy, nibabel and requests, and Colab already ships all three. The pin numpy>=2.5.1 would otherwise make pip upgrade Colab's numpy, which is the kind of breakage the --no-deps installs are there to avoid.

Notebooks that run a plain pip install MRzeroCore already get bifti and are unchanged.


Generated by Claude Code

…no-deps

MRzeroCore 1.3 depends on bifti, which is not pulled in when the
notebooks install MRzeroCore with --no-deps. bifti is installed with
--no-deps as well, since its requirements (numpy, nibabel, requests)
are already present in Colab and should not be upgraded.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NHKPBZR1HP47yhA3BKxHT4
bifti (installed by the notebooks with --no-deps) imports nibabel, which
Colab ships but the CI runner does not.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NHKPBZR1HP47yhA3BKxHT4
@J-Endres
J-Endres merged commit 2dca7ac into main Oct 28, 2026
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@J-Endres
J-Endres deleted the claude/confident-wozniak-old4ba branch October 28, 2026 14:04
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github-actions Bot commented Oct 28, 2026 •

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Simulation test: main (before) vs. this PR (after)

Sequence Status max mag NRMSE max phase RMSE max runtime Δ
mr0_DREAM_STE_seq ✅ 0.00e+00 0.00e+00 +4.0%
mr0_DWI_SE_EPI ✅ 0.00e+00 0.00e+00 +3.7%
mr0_EPI_2D_seq ✅ 0.00e+00 0.00e+00 +4.7%
mr0_FID_seq ✅ 0.00e+00 0.00e+00 +0.6%
mr0_FLASH_2D_seq ✅ 0.00e+00 0.00e+00 +5.0%
mr0_GRE_to_FLASH ⚠️ – – –
mr0_RARE_2D_seq ✅ 0.00e+00 0.00e+00 +6.6%
mr0_SE_CPMG_seq ✅ 0.00e+00 0.00e+00 +4.9%
mr0_STE_3pulses_5echoes_seq ✅ 6.86e-09 1.49e-08 +7.5%
mr0_TSE_2D_multi_shot_seq ✅ 0.00e+00 0.00e+00 +1.6%
mr0_bSSFP_2D_seq ✅ 0.00e+00 0.00e+00 +2.2%
mr0_diffusion_prep_STEAM_2D_seq ✅ 0.00e+00 0.00e+00 +16.2%
✅ mr0_DREAM_STE_seq: All tests passed.

mr0_DREAM_STE_seq

✅ mr0_DWI_SE_EPI: All tests passed.

mr0_DWI_SE_EPI

✅ mr0_EPI_2D_seq: All tests passed.

mr0_EPI_2D_seq

✅ mr0_FID_seq: All tests passed.

mr0_FID_seq

✅ mr0_FLASH_2D_seq: All tests passed.

mr0_FLASH_2D_seq

⚠️ mr0_GRE_to_FLASH: No comparison possible: [Errno 2] No such file or directory: '/home/runner/work/MRzero-Core/MRzero-Core/tests/simulation_test/ref_files/mr0_GRE_to_FLASH.seq.npz'
✅ mr0_RARE_2D_seq: All tests passed.

mr0_RARE_2D_seq

✅ mr0_SE_CPMG_seq: All tests passed.

mr0_SE_CPMG_seq

✅ mr0_STE_3pulses_5echoes_seq: All tests passed.

mr0_STE_3pulses_5echoes_seq

✅ mr0_TSE_2D_multi_shot_seq: All tests passed.

mr0_TSE_2D_multi_shot_seq

✅ mr0_bSSFP_2D_seq: All tests passed.

mr0_bSSFP_2D_seq

✅ mr0_diffusion_prep_STEAM_2D_seq: All tests passed.

mr0_diffusion_prep_STEAM_2D_seq

Workflow run — raw .npz data is attached as artifacts.

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